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"https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143736974" }, { "id": "rs143736974", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143736974" }, { "id": "rs143736974", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143736974" }, { "id": "rs143736974", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143736974#frequency_tab" }, { "id": "rs143736974", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143736974" } ], "glycoeffect": [], "start_pos": 786, "end_pos": 786, "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21879108", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N786", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:0090032", "recommended_name": { "id": "DOID:0090032", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090032", "name": "Silverman-Handmaker type dyssegmental dysplasia", "description": "An osteochondrodysplasia characterized by short-limbed dwarfism, anisospondyly, and neonatal lethality that has_material_basis_in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the gene encoding perlecan (HSPG2) on chromosome 1p36." }, "synonyms": [ { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "Silverman-Handmaker type dyssegmental dysplasia", "description": "Dyssegmental dysplasia, Silverman-Handmaker type is a rare, genetic, primary bone dysplasia, and lethal form of neonatal short-limbed dwarfism, characterized by anisospondyly, severe short stature and limb shortening, metaphyseal flaring and distinct dysmorphic features (i.e. flat facial appearance, abnormal ears, short neck, narrow thorax). Additional features may include other skeletal findings (e.g. joint contractures, bowed limbs, talipes equinovarus) and urogenital and cardiovascular abnormalities." }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "Anisospondylic camptomicromelic dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "DDSH", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dysplasia Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dysplasia, Silverman-Handmaker type", "description": "" }, { "id": "MIM:224410", "resource": "MIM", "url": "https://www.omim.org/entry/224410", "name": "Dyssegmental dysplasia Silverman-Handmaker type", "description": "Dyssegmental dysplasia Silverman-Handmaker type" } ], "unlinked_id_list": [], "evidence": [ { "id": "224410", "database": "MIM", "url": "https://www.omim.org/entry/224410" }, { "id": "0090032", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0090032" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs769088707", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769088707" }, { "id": "rs769088707", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769088707" }, { "id": "rs769088707", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769088707#frequency_tab" }, { "id": "rs769088707", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769088707" } ], "glycoeffect": [], "start_pos": 786, "end_pos": 786, "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21879109", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N786", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P98160", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" }, { "id": "rs758631172", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758631172" }, { "id": "rs758631172", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758631172" }, { "id": "rs758631172", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758631172#frequency_tab" }, { "id": "rs758631172", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758631172" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 787, "end_pos": 787, "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21879105", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T787", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - 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Additional features may include other skeletal findings (e.g. joint contractures, bowed limbs, talipes equinovarus) and urogenital and cardiovascular abnormalities." }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "Anisospondylic camptomicromelic dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "DDSH", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dysplasia Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dysplasia, Silverman-Handmaker type", "description": "" }, { "id": "MIM:224410", "resource": "MIM", "url": "https://www.omim.org/entry/224410", "name": "Dyssegmental dysplasia Silverman-Handmaker type", "description": "Dyssegmental dysplasia Silverman-Handmaker type" } ], "unlinked_id_list": [], "evidence": [ { "id": "224410", "database": "MIM", "url": "https://www.omim.org/entry/224410" }, { "id": "0090032", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0090032" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P98160", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" }, { "id": "rs760187334", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760187334" }, { "id": "rs760187334", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760187334" }, { "id": "rs760187334", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760187334#frequency_tab" }, { "id": "rs760187334", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760187334" } ], "glycoeffect": [], "start_pos": 882, "end_pos": 882, "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21878227", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R882", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs775214005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775214005" }, { "id": "rs775214005", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775214005" }, { "id": "rs775214005", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775214005#frequency_tab" }, { "id": "rs775214005", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775214005" } ], "glycoeffect": [], "start_pos": 882, "end_pos": 882, "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21878226", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R882", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P98160", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" } ], "glycoeffect": [], "start_pos": 882, "end_pos": 882, "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21878226", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R882", "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": "P98160", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" } ], "glycoeffect": [], "start_pos": 883, "end_pos": 883, "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21878223", "ref_nt": "C", "alt_nt": "T", 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"https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", 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"https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" } ], "glycoeffect": [], "start_pos": 885, "end_pos": 885, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21878216", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M885", "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": "rs1426721029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1426721029" }, { "id": "rs1426721029", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1426721029#frequency_tab" }, { "id": "rs1426721029", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1426721029" } ], "glycoeffect": [], "start_pos": 885, "end_pos": 885, "sequence_org": "M", "sequence_mut": "T", "comment": 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"o-glyco-site-loss" ], "start_pos": 887, "end_pos": 887, "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21878211", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T887", "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": 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"DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": 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"description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1641232595", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1641232595" }, { "id": "rs1641232595", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1641232595#frequency_tab" } ], "glycoeffect": [], "start_pos": 890, "end_pos": 890, "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21878203", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E890", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748259811", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748259811" }, { "id": "rs748259811", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748259811" }, { "id": "rs748259811", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748259811" } ], "glycoeffect": [], "start_pos": 891, "end_pos": 891, "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21878200", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A891", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748259811", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748259811" }, { "id": "rs748259811", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748259811" }, { "id": "rs748259811", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748259811" } ], "glycoeffect": [], "start_pos": 891, "end_pos": 891, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21878200", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A891", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781183475", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781183475" }, { "id": "rs781183475", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781183475" }, { "id": "rs781183475", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781183475#frequency_tab" }, { "id": "rs781183475", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781183475" } ], "glycoeffect": [], "start_pos": 892, "end_pos": 892, "sequence_org": "C", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21878196", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C892", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781183475", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781183475" }, { "id": "rs781183475", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781183475" }, { "id": "rs781183475", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781183475#frequency_tab" }, { "id": "rs781183475", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781183475" } ], "glycoeffect": [], "start_pos": 892, "end_pos": 892, "sequence_org": "C", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21878196", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C892", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755094755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755094755" }, { "id": "rs755094755", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755094755" }, { "id": "rs755094755", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755094755#frequency_tab" }, { "id": "rs755094755", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755094755" } ], "glycoeffect": [], "start_pos": 893, "end_pos": 893, "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21878194", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R893", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P98160", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" }, { "id": "rs751663070", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751663070" }, { "id": "rs751663070", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751663070" }, { "id": "rs751663070", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751663070#frequency_tab" }, { "id": "rs751663070", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751663070" } ], "glycoeffect": [], "start_pos": 893, "end_pos": 893, "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21878193", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R893", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" 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Additional features may include other skeletal findings (e.g. joint contractures, bowed limbs, talipes equinovarus) and urogenital and cardiovascular abnormalities." }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "Anisospondylic camptomicromelic dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "DDSH", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dysplasia Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": 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"Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Aberfeld syndrome", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Burton skeletal dysplasia", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Burton syndrome", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Catel-Hempel syndrome", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Schwartz-Jampel syndrome type 1", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Schwartz-Jampel-Aberfeld syndrome", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Catel-Hempel type dysostosis enchondralis metaepiphysaria", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "myotonic chondrodystrophy", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "osteochondromuscular dystrophy", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "myotonic myopathy, dwarfism, chondrodystrophy, ocular and facial anomalies", "description": "" }, { "id": "MONDO:0100435", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100435", "name": "Schwartz-Jampel syndrome type 1", "description": "" }, { "id": "MONDO:0100435", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100435", "name": "SJA syndrome", "description": "" }, { "id": "MONDO:0100435", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100435", "name": "SJS1", "description": "" }, { "id": "MONDO:0100435", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100435", "name": "Schwartz-Jampel syndrome type 1", "description": "" }, { "id": "MONDO:0100435", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100435", "name": "Schwartz-Jampel syndrome, type 1", "description": "" }, { "id": "MIM:255800", "resource": "MIM", "url": "https://www.omim.org/entry/255800", "name": "Schwartz-Jampel syndrome", "description": "Schwartz-Jampel syndrome" } ], "unlinked_id_list": [], "evidence": [ { "id": "255800", "database": "MIM", "url": "https://www.omim.org/entry/255800" }, { "id": "0090005", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0090005" } ] } ] }, { "evidence": [ { "id": "rs1642292393", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1642292393" }, { "id": "rs1642292393", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1642292393" } ], "glycoeffect": [], "start_pos": 90, "end_pos": 90, "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21890669", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F90", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1469910143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1469910143" }, { "id": "rs1469910143", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1469910143#frequency_tab" }, { "id": "rs1469910143", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1469910143" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 910, "end_pos": 910, "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21876609", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S910", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P98160", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" } ], "glycoeffect": [], "start_pos": 911, "end_pos": 911, "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21876605", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "F911", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain 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"https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" }, { "id": "rs1572329473", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572329473" }, { "id": "rs1572329473", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572329473" } ], "glycoeffect": [], "start_pos": 912, "end_pos": 912, "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "P", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21876603", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "H912", "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": 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"DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "Catel-Hempel type dysostosis enchondralis metaepiphysaria", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "myotonic chondrodystrophy", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "osteochondromuscular dystrophy", "description": "" }, { "id": "DOID:0090005", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090005", "name": "myotonic myopathy, dwarfism, chondrodystrophy, ocular and facial anomalies", "description": "" }, { "id": "MONDO:0100435", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0100435", "name": "Schwartz-Jampel syndrome type 1", "description": "" }, { "id": "MONDO:0100435", "resource": "MONDO", "url": 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"sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21876546", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R931", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the 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"start_pos": 934, "end_pos": 934, "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21876539", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T934", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P98160", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98160" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 935, "end_pos": 935, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 0 out of 6 filters: .", "chr_id": "1", "chr_pos": "21876533", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S935", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", 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"comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21876336", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E966", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0090032", "recommended_name": { "id": "DOID:0090032", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090032", "name": "Silverman-Handmaker type dyssegmental dysplasia", "description": "An osteochondrodysplasia characterized by short-limbed dwarfism, anisospondyly, and neonatal lethality that has_material_basis_in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the gene encoding perlecan (HSPG2) on chromosome 1p36." }, "synonyms": [ { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "Silverman-Handmaker type dyssegmental dysplasia", "description": "Dyssegmental 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"url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/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:0090032", "recommended_name": { "id": "DOID:0090032", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0090032", "name": "Silverman-Handmaker type dyssegmental dysplasia", "description": "An osteochondrodysplasia characterized by short-limbed dwarfism, anisospondyly, and neonatal lethality that has_material_basis_in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the gene encoding perlecan (HSPG2) on chromosome 1p36." }, "synonyms": [ { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "Silverman-Handmaker type dyssegmental dysplasia", "description": "Dyssegmental dysplasia, Silverman-Handmaker type is a rare, genetic, primary bone dysplasia, and lethal form of neonatal short-limbed dwarfism, characterized by anisospondyly, severe short stature and limb shortening, metaphyseal flaring and distinct dysmorphic features (i.e. flat facial appearance, abnormal ears, short neck, narrow thorax). Additional features may include other skeletal findings (e.g. joint contractures, bowed limbs, talipes equinovarus) and urogenital and cardiovascular abnormalities." }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "Anisospondylic camptomicromelic dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "DDSH", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dwarfism Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dysplasia Silverman-Handmaker type", "description": "" }, { "id": "MONDO:0009140", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009140", "name": "dyssegmental dysplasia, Silverman-Handmaker type", "description": "" }, { "id": "MIM:224410", "resource": "MIM", "url": "https://www.omim.org/entry/224410", "name": "Dyssegmental dysplasia Silverman-Handmaker type", "description": "Dyssegmental dysplasia Silverman-Handmaker type" } ], "unlinked_id_list": [], "evidence": [ { "id": "224410", "database": "MIM", "url": "https://www.omim.org/entry/224410" }, { "id": "0090032", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0090032" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs139374562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139374562" }, { "id": "rs139374562", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs139374562" }, { "id": "rs139374562", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139374562" }, { "id": "rs139374562", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139374562#frequency_tab" }, { "id": "rs139374562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139374562" } ], "glycoeffect": [], "start_pos": 999, "end_pos": 999, "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21876236", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "G999", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1174633773", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1174633773" }, { "id": "rs1174633773", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1174633773" } ], "glycoeffect": [], "start_pos": 999, "end_pos": 999, "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21876237", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G999", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1289486927", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289486927" }, { "id": "rs1289486927", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1289486927#frequency_tab" } ], "glycoeffect": [], "start_pos": 9, "end_pos": 9, "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, gag-related.", "chr_id": "1", "chr_pos": "21937192", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L9", "keywords": [ "ebi", "germline" ] } ] } }