{ "uniprot_canonical_ac": "P05997-1", "uniprot_ac": "P05997", "uniprot_id": "CO5A2_HUMAN", "mass": { "chemical_mass": 144910.0, "monoisotopic_mass": 144910.0 }, "refseq": { "ac": "NP_000384", "name": "collagen alpha-2(V) chain preproprotein", "summary": "This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. [provided by RefSeq, Jul 2008].", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384" }, "gene_names": [ { "name": "COL5A2", "resource": "UniProtKB", "type": "recommended", "url": "https://www.uniprot.org/uniprot/P05997", "id": "P05997" }, { "name": "COL5A2", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384", "id": "NP_000384" }, { "name": "EDSC; EDSCL2", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384", "id": "NP_000384" } ], "protein_names": [ { "name": "Collagen alpha-2(V) chain", "resource": "UniProtKB", "type": "recommended", "url": "", "id": "P05997" }, { "name": "AB collagen; collagen, fetal membrane, A polypeptide; collagen alpha-2(V) chain; type V preprocollagen alpha 2 chain", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384", "id": "NP_000384" }, { "name": "collagen alpha-2(V) chain preproprotein", "resource": "RefSeq", "type": "synonym", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384", "id": "NP_000384" } ], "function": [ { "annotation": "Collagen type V alpha 2 promotes the development of gastric cancer via M2 macrophage polarization.", "evidence": [ { "database": "RefSeq", "id": "NP_000384", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384" }, { "database": "PubMed", "id": "37082997", "url": "https://glygen.org/publication/PubMed/37082997" } ] }, { "annotation": "LncRNA BZRAP1-AS1 alleviates rheumatoid arthritis by regulating miR-1286/COL5A2 axis.", "evidence": [ { "database": "RefSeq", "id": "NP_000384", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384" }, { "database": "PubMed", "id": "34766472", "url": "https://glygen.org/publication/PubMed/34766472" } ] }, { "annotation": "Phenotype of COL3A1/COL5A2 deletion patients.", "evidence": [ { "database": "RefSeq", "id": "NP_000384", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384" }, { "database": "PubMed", "id": "35964930", "url": "https://glygen.org/publication/PubMed/35964930" } ] }, { "annotation": "Rare functional genetic variants in COL7A1, COL6A5, COL1A2 and COL5A2 frequently occur in Chiari Malformation Type 1. Publication Status: Online-Only", "evidence": [ { "database": "RefSeq", "id": "NP_000384", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384" }, { "database": "PubMed", "id": "33974636", "url": "https://glygen.org/publication/PubMed/33974636" } ] }, { "annotation": "This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. [provided by RefSeq, Jul 2008].", "evidence": [ { "database": "RefSeq", "id": "NP_000384", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_000384" } ] }, { "annotation": "Type V collagen is a member of group I collagen (fibrillar forming collagen). It is a minor connective tissue component of nearly ubiquitous distribution. Type V collagen binds to DNA, heparan sulfate, thrombospondin, heparin, and insulin. Type V collagen is a key determinant in the assembly of tissue-specific matrices (By similarity).", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997#function" } ] } ], "disease": [ { "disease_id": "DOID:0080726", "recommended_name": { "id": "DOID:0080726", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:0080726", "name": "Ehlers-Danlos syndrome classic type 2", "description": "An Ehlers-Danlos syndrome that has_material_basis_in heterozygous mutation in the collagen alpha-2(V) gene on chromosome 2q31 and that is characterized by the absence of widened atrophic scars." }, "synonyms": [ { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, classic type, 2", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A2 gene." }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "EDS II", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "EDSCL2", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, classic type, 2", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "EDS II, formerly", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mild Classic type", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mild Classic type, formerly", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mitis type", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mitis type, formerly", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, type Ii", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, type Ii, formerly", "description": "" }, { "id": "MIM:130010", "resource": "MIM", "url": "https://www.omim.org/entry/130010", "name": "Ehlers-Danlos syndrome, classic type, 2", "description": "Ehlers-Danlos syndrome, classic type, 2" } ], "evidence": [ { "id": "130010", "database": "MIM", "url": "https://www.omim.org/entry/130010" } ] } ], "snv": [ { "evidence": [ { "id": "rs1171565895", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171565895" }, { "id": "rs1171565895", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171565895" }, { "id": "rs1200980765", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200980765" }, { "id": "rs1200980765", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1200980765#frequency_tab" }, { "id": "rs1200980765", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1200980765" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1015, "end_pos": 1015, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 out of 1 filters: o-glyco-site-loss (T->I).", "chr_id": "2", "chr_pos": "189035064", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1015", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1200980765", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200980765" }, { "id": "rs1200980765", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1200980765#frequency_tab" }, { "id": "rs1200980765", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1200980765" } ], "glycoeffect": [ "o-glyco-site-loss" ], "start_pos": 1015, "end_pos": 1015, "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 out of 1 filters: o-glyco-site-loss (T->K).", "chr_id": "2", "chr_pos": "189049450", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1015", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" }, { "id": "rs1576486531", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1576486531" }, { "id": "rs1576486531", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1576486531" }, { "id": "22197931", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22197931" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1241, "end_pos": 1241, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DES->NES).", "chr_id": "2", "chr_pos": "189039476", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1241", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://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": "http://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs1250787856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250787856" }, { "id": "rs1250787856", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250787856" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 1262, "end_pos": 1262, "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NKT->KKT).", "chr_id": "2", "chr_pos": "189039411", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1262", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766139391", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766139391" }, { "id": "rs766139391", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766139391" }, { "id": "rs766139391", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766139391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 1262, "end_pos": 1262, "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NKT->SKT).", "chr_id": "2", "chr_pos": "189039412", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1262", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" }, { "id": "rs762902468", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762902468" }, { "id": "rs762902468", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762902468" }, { "id": "rs762902468", "database": "NCI-TCGA", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762902468" }, { "id": "rs762902468", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762902468#frequency_tab" }, { "id": "rs762902468", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762902468" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "start_pos": 1264, "end_pos": 1264, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-loss (NKT->NKM).", "chr_id": "2", "chr_pos": "189039406", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1264", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ] }, { "disease_id": "DOID:13359", "recommended_name": { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "Ehlers-Danlos syndrome", "description": "A collagen disease that is characterized by extremely flexible joints, elastic skin, and excessive bruising caused by a heritable defect in collagen synthesis, which leads to marked healing difficulties. EDS has five cardinal signs, which may be present to some degree in all of the subtypes. These five cardinal signs are skin fragility, blood vessel fragility, skin hyperelasticity, joint hypermobility, and characteristic subcutaneous nodules." }, "synonyms": [ { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "Cutis hyperelastica", "description": "" }, { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "elastic skin", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A1 gene." }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDS I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] }, { "disease_id": "DOID:14720", "recommended_name": { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome classic type 1", "description": "An Ehlers-Danlos syndrome that is characterized by loose-jointedness and fragile, bruisable skin that heals with peculiar 'cigarette-paper' scars and that has_material_basis_in heterozygous mutation in the collagen alpha-1(V) gene (COL5A1) on chromosome 9q34." }, "synonyms": [ { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A1 gene." }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDS I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] }, { "disease_id": "DOID:0080726", "recommended_name": { "id": "DOID:0080726", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:0080726", "name": "Ehlers-Danlos syndrome classic type 2", "description": "An Ehlers-Danlos syndrome that has_material_basis_in heterozygous mutation in the collagen alpha-2(V) gene on chromosome 2q31 and that is characterized by the absence of widened atrophic scars." }, "synonyms": [ { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, classic type, 2", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A2 gene." }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "EDS II", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "EDSCL2", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, classic type, 2", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "EDS II, formerly", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mild Classic type", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mild Classic type, formerly", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mitis type", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers Danlos syndrome, mitis type, formerly", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, type Ii", "description": "" }, { "id": "MONDO:0019568", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019568", "name": "Ehlers-Danlos syndrome, type Ii, formerly", "description": "" }, { "id": "MIM:130010", "resource": "MIM", "url": "https://www.omim.org/entry/130010", "name": "Ehlers-Danlos syndrome, classic type, 2", "description": "Ehlers-Danlos syndrome, classic type, 2" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1269, "end_pos": 1269, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (HAT->NAT).", "chr_id": "2", "chr_pos": "189039392", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H1269", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" }, { "id": "rs1194645204", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194645204" }, { "id": "rs1194645204", "database": "NCI-TCGA", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194645204" }, { "id": "rs1194645204", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194645204#frequency_tab" }, { "id": "rs1194645204", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194645204" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1286, "end_pos": 1286, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (DGS->NGS).", "chr_id": "2", "chr_pos": "189039341", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1286", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, intestinal", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ] }, { "disease_id": "DOID:13359", "recommended_name": { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "Ehlers-Danlos syndrome", "description": "A collagen disease that is characterized by extremely flexible joints, elastic skin, and excessive bruising caused by a heritable defect in collagen synthesis, which leads to marked healing difficulties. EDS has five cardinal signs, which may be present to some degree in all of the subtypes. These five cardinal signs are skin fragility, blood vessel fragility, skin hyperelasticity, joint hypermobility, and characteristic subcutaneous nodules." }, "synonyms": [ { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "Cutis hyperelastica", "description": "" }, { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "elastic skin", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A1 gene." }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDS I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] }, { "disease_id": "DOID:14720", "recommended_name": { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome classic type 1", "description": "An Ehlers-Danlos syndrome that is characterized by loose-jointedness and fragile, bruisable skin that heals with peculiar 'cigarette-paper' scars and that has_material_basis_in heterozygous mutation in the collagen alpha-1(V) gene (COL5A1) on chromosome 9q34." }, "synonyms": [ { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A1 gene." }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDS I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1351723313", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1351723313" }, { "id": "rs1351723313", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1351723313" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1341, "end_pos": 1341, "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (NPS->NLS).", "chr_id": "2", "chr_pos": "189036707", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1341", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1341, "end_pos": 1341, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NPS->NSS).", "chr_id": "2", "chr_pos": "189036708", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1341", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "A thoracic cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "http://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": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, familial", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, familial Male", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs979486002", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs979486002" }, { "id": "rs979486002", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs979486002" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "start_pos": 1400, "end_pos": 1400, "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NIT->KIT).", "chr_id": "2", "chr_pos": "189035069", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1400", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1171565895", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171565895" }, { "id": "rs1171565895", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171565895" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "start_pos": 1402, "end_pos": 1402, "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-loss (NIT->NII).", "chr_id": "2", "chr_pos": "189035064", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1402", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" } ], "glycoeffect": [], "start_pos": 1414, "end_pos": 1414, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 out of 6 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "189035029", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1414", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://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": "http://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1436390158", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1436390158" }, { "id": "rs1436390158", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1436390158#frequency_tab" }, { "id": "rs1436390158", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1436390158" }, { "id": "22980975", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22980975" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1440, "end_pos": 1440, "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 out of 1 filters: n-glyco-sequon-gain (NIR->NIS).", "chr_id": "2", "chr_pos": "189034949", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1440", "disease": [ { "disease_id": "DOID:13359", "recommended_name": { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "Ehlers-Danlos syndrome", "description": "A collagen disease that is characterized by extremely flexible joints, elastic skin, and excessive bruising caused by a heritable defect in collagen synthesis, which leads to marked healing difficulties. EDS has five cardinal signs, which may be present to some degree in all of the subtypes. These five cardinal signs are skin fragility, blood vessel fragility, skin hyperelasticity, joint hypermobility, and characteristic subcutaneous nodules." }, "synonyms": [ { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "Cutis hyperelastica", "description": "" }, { "id": "DOID:13359", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:13359", "name": "elastic skin", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A1 gene." }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDS I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] }, { "disease_id": "DOID:14720", "recommended_name": { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome classic type 1", "description": "An Ehlers-Danlos syndrome that is characterized by loose-jointedness and fragile, bruisable skin that heals with peculiar 'cigarette-paper' scars and that has_material_basis_in heterozygous mutation in the collagen alpha-1(V) gene (COL5A1) on chromosome 9q34." }, "synonyms": [ { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A1 gene." }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDS I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs550723518", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs550723518" }, { "id": "rs550723518", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs550723518" }, { "id": "rs550723518", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs550723518" }, { "id": "rs550723518", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs550723518" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 1449, "end_pos": 1449, "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (TCS->NCS).", "chr_id": "2", "chr_pos": "189034923", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.0002", "site_lbl": "T1449", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1456, "end_pos": 1456, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NGN->NGS).", "chr_id": "2", "chr_pos": "189034203", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N1456", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://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": "http://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs778927121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778927121" }, { "id": "rs778927121", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778927121" }, { "id": "rs778927121", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778927121" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1458, "end_pos": 1458, "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (NVG->NVS).", "chr_id": "2", "chr_pos": "189034198", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1458", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" }, { "id": "rs753194366", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753194366" }, { "id": "rs753194366", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753194366" }, { "id": "rs753194366", "database": "NCI-TCGA", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753194366" }, { "id": "rs753194366", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753194366" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 1470, "end_pos": 1470, "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 out of 6 filters: n-glyco-sequon-gain (NVA->NVT).", "chr_id": "2", "chr_pos": "189034162", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1470", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P05997", "database": "BioMuta", "url": "https://hive.biochemistry.gwu.edu/biomuta/proteinview/P05997" } ], "glycoeffect": [], "start_pos": 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"https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] }, { "disease_id": "DOID:14720", "recommended_name": { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome classic type 1", "description": "An Ehlers-Danlos syndrome that is characterized by loose-jointedness and fragile, bruisable skin that heals with peculiar 'cigarette-paper' scars and that has_material_basis_in heterozygous mutation in the collagen alpha-1(V) gene (COL5A1) on chromosome 9q34." }, "synonyms": [ { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "DOID:14720", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:14720", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Any Ehlers-Danlos syndrome in which the cause of the disease is a mutation in the COL5A1 gene." }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDS I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "EDSCL1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type 1", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "Ehlers-Danlos syndrome, type I", "description": "" }, { "id": "MONDO:0019567", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0019567", "name": "type I Ehlers-Danlos syndrome", "description": "" }, { "id": "MIM:130000", "resource": "MIM", "url": "https://www.omim.org/entry/130000", "name": "Ehlers-Danlos syndrome, classic type, 1", "description": "Ehlers-Danlos syndrome, classic type, 1" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs372910621", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372910621" }, { "id": "rs372910621", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372910621" }, { "id": "rs372910621", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372910621#frequency_tab" }, { "id": "rs372910621", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372910621" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 6, "end_pos": 6, "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (NWA->NWT).", "chr_id": "2", "chr_pos": "189179589", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A6", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs769655969", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769655969" }, { "id": "rs769655969", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769655969" }, { "id": "rs769655969", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769655969" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "start_pos": 743, "end_pos": 743, "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (KGS->NGS).", "chr_id": "2", "chr_pos": "189043232", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K743", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1251112610", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1251112610" }, { "id": "rs1251112610", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1251112610#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "start_pos": 841, "end_pos": 841, "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 out of 1 filters: n-glyco-sequon-gain (NGP->NGS).", "chr_id": "2", "chr_pos": "189053456", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P841", "keywords": [ "ebi", "germline" ] } ], "mutagenesis": [], "expression_tissue": [ { "tissue": { "name": "Adult mammalian kidney", "namespace": "UBERON", "id": "0000082", "url": "http://purl.obolibrary.org/obo/UBERON_0000082" }, "score": "72.7", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Oral cavity", "namespace": "UBERON", "id": "0000167", "url": "http://purl.obolibrary.org/obo/UBERON_0000167" }, "score": "82.04", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Stomach", "namespace": "UBERON", "id": "0000945", "url": "http://purl.obolibrary.org/obo/UBERON_0000945" }, "score": "88.26", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Uterus", "namespace": "UBERON", "id": "0000995", "url": "http://purl.obolibrary.org/obo/UBERON_0000995" }, "score": "89.07", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Esophagus", "namespace": "UBERON", "id": "0001043", "url": "http://purl.obolibrary.org/obo/UBERON_0001043" }, "score": "96.05", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Rectum", "namespace": "UBERON", "id": "0001052", "url": "http://purl.obolibrary.org/obo/UBERON_0001052" }, "score": "91.09", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Colon", "namespace": "UBERON", "id": "0001155", "url": "http://purl.obolibrary.org/obo/UBERON_0001155" }, "score": "80.04", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Urinary bladder", "namespace": "UBERON", "id": "0001255", "url": "http://purl.obolibrary.org/obo/UBERON_0001255" }, "score": "92.73", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Thyroid gland", "namespace": "UBERON", "id": "0002046", "url": "http://purl.obolibrary.org/obo/UBERON_0002046" }, "score": "82.51", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Lung", "namespace": "UBERON", "id": "0002048", "url": "http://purl.obolibrary.org/obo/UBERON_0002048" }, "score": "87.45", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Liver", "namespace": "UBERON", "id": "0002107", "url": "http://purl.obolibrary.org/obo/UBERON_0002107" }, "score": "80.88", "present": "MEDIUM", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Prostate gland", "namespace": "UBERON", "id": "0002367", "url": "http://purl.obolibrary.org/obo/UBERON_0002367" }, "score": "83.07", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] }, { "tissue": { "name": "Thoracic mammary gland", "namespace": "UBERON", "id": "0005200", "url": "http://purl.obolibrary.org/obo/UBERON_0005200" }, "score": "90.05", "present": "HIGH", "evidence": [ { "database": "Bgee", "id": "ENSG00000204262", "url": "https://bgee.org/?page=gene&gene_id=ENSG00000204262" } ] } ], "expression_disease": [ { "significant": "No", "trend": "up", "name": "Prostate cancer [DO disease name]", "url": "http://disease-ontology.org/term/DOID:10283", "evidence": [ { "database": "BioXpress", "id": "P05997", "url": "https://hive.biochemistry.gwu.edu/bioxpress/transcriptview/P05997" } ], "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://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": "http://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease 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"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: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": 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"https://monarchinitiative.org/disease/MONDO:0023122", "name": "hereditary prostate cancer", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "hereditary prostate carcinoma", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, familial, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, somatic", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "prostate cancer, 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"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:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "Prca1", "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: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:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer susceptibility, X-linked", "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": "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:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" } ] } ] }, { "significant": "Yes", "trend": "up", "name": "Stomach cancer [DO disease name]", "url": "http://disease-ontology.org/term/DOID:10534", "evidence": [ { "database": "BioXpress", "id": "P05997", "url": "https://hive.biochemistry.gwu.edu/bioxpress/transcriptview/P05997" } ], "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { 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"" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "adenocarcinoma of lung, susceptibility to", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": 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"MMANWAEARPLLILIVLLGQFVSIKAQEEDEDEGYGEEIACTQNGQMYLNRDIWKPAPCQICVCDNGAILCDKIECQDVLDCADPVTPPGECCPVCSQTPGGGNTNFGRGRKGQKGEPGLVPVVTGIRGRPGPAGPPGSQGPRGERGPKGRPGPRGPQGIDGEPGVPGQPGAPGPPGHPSHPGPDGLSRPFSAQMAGLDEKSGLGSQVGLMPGSVGPVGPRGPQGLQGQQGGAGPTGPPGEPGDPGPMGPIGSRGPEGPPGKPGEDGEPGRNGNPGEVGFAGSPGARGFPGAPGLPGLKGHRGHKGLEGPKGEVGAPGSKGEAGPTGPMGAMGPLGPRGMPGERGRLGPQGAPGQRGAHGMPGKPGPMGPLGIPGSSGFPGNPGMKGEAGPTGARGPEGPQGQRGETGPPGPVGSPGLPGAIGTDGTPGAKGPTGSPGTSGPPGSAGPPGSPGPQGSTGPQGIRGQPGDPGVPGFKGEAGPKGEPGPHGIQGPIGPPGEEGKRGPRGDPGTVGPPGPVGERGAPGNRGFPGSDGLPGPKGAQGERGPVGSSGPKGSQGDPGRPGEPGLPGARGLTGNPGVQGPEGKLGPLGAPGEDGRPGPPGSIGIRGQPGSMGLPGPKGSSGDPGKPGEAGNAGVPGQRGAPGKDGEVGPSGPVGPPGLAGERGEQGPPGPTGFQGLPGPPGPPGEGGKPGDQGVPGDPGAVGPLGPRGERGNPGERGEPGITGLPGEKGMAGGHGPDGPKGSPGPSGTPGDTGPPGLQGMPGERGIAGTPGPKGDRGGIGEKGAEGTAGNDGARGLPGPLGPPGPAGPTGEKGEPGPRGLVGPPGSRGNPGSRGENGPTGAVGFAGPQGPDGQPGVKGEPGEPGQKGDAGSPGPQGLAGSPGPHGPNGVPGLKGGRGTQGPPGATGFPGSAGRVGPPGPAGAPGPAGPLGEPGKEGPPGLRGDPGSHGRVGDRGPAGPPGGPGDKGDPGEDGQPGPDGPPGPAGTTGQRGIVGMPGQRGERGMPGLPGPAGTPGKVGPTGATGDKGPPGPVGPPGSNGPVGEPGPEGPAGNDGTPGRDGAVGERGDRGDPGPAGLPGSQGAPGTPGPVGAPGDAGQRGDPGSRGPIGPPGRAGKRGLPGPQGPRGDKGDHGDRGDRGQKGHRGFTGLQGLPGPPGPNGEQGSAGIPGPFGPRGPPGPVGPSGKEGNPGPLGPIGPPGVRGSVGEAGPEGPPGEPGPPGPPGPPGHLTAALGDIMGHYDESMPDPLPEFTEDQAAPDDKNKTDPGVHATLKSLSSQIETMRSPDGSKKHPARTCDDLKLCHSAKQSGEYWIDPNQGSVEDAIKVYCNMETGETCISANPSSVPRKTWWASKSPDNKPVWYGLDMNRGSQFAYGDHQSPNTAITQMTFLRLLSKEASQNITYICKNSVGYMDDQAKNLKKAVVLKGANDLDIKAEGNIRFRYIVLQDTCSKRNGNVGKTVFEYRTQNVARLPIIDLAPVDVGGTDQEFGVEIGPVCFV", "length": 1499, "header": "sp|P05997-1|CO5A2_HUMAN Isoform 1 of Collagen alpha-2(V) chain OS=Homo sapiens OX=9606 GN=COL5A2 PE=1 SV=3 CANONICAL=P05997-1" }, "isoforms": [ { "isoform_ac": "A0A087WYX9-1", "url": "", "sequence": { "sequence": "MPGSVGPVGPRGPQGLQGQQGGAGPTGPPGEPGDPGPMGPIGSRGPEGPPGKPGEDGEPGRNGNPGEVGFAGSPGARGFPGAPGLPGLKGHRGHKGLEGPKGEVGAPGSKGEAGPTGPMGDPGTVGPPGPVGERGAPGNRGFPGSDGLPGPKGAQGERGPVGSSGPKGSQGDPGRPGEPGLPGARGLTGNPGVQGPEGKLGPLGAPGEDGRPGPPGSIGIRGQPGSMGLPGPKGSSGDPGKPGEAGNAGVPGQRGAPGKDGEVGPSGPVGPPGLAGERGEQGPPGPTGFQGLPGPPGPPGEGGKPGDQGVPGDPGAVGPLGPRGERGNPGERGEPGITGLPGEKGMAGGHGPDGPKGSPGPSGTPGDTGPPGLQGMPGERGIAGTPGPKGDRGGIGEKGAEGTAGNDGARGLPGPLGPPGPAGPTGEKGEPGPRGLVGPPGSRGNPGSRGENGPTGAVGFAGPQGPDGQPGVKGEPGEPGQKGDAGSPGPQGLAGSPGPHGPNGVPGLKGGRGTQGPPGATGFPGSAGRVGPPGPAGAPGPAGPLGEPGKEGPPGLRGDPGSHGRVGDRGPAGPPGGPGDKGDPGEDGQPGPDGPPGPAGTTGQRGIVGMPGQRGERGMPGLPGPAGTPGKVGPTGATGDKGPPGPVGPPGSNGPVGEPGPEGPAGNDGTPGRDGAVGERGDRGDPGPAGLPGSQGAPGTPGPVGAPGDAGQRGDPGSRGPIGPPGRAGKRGLPGPQGPRGDKGDHGDRGDRGQKGHRGFTGLQGLPGPPGPNGEQGSAGIPGPFGPRGPPGPVGPSGKEGNPGPLGPIGPPGVRGSVGEAGPEGPPGEPGPPGPPGPPGHLTAALGDIMGHYDESMPDPLPEFTEDQAAPDDKNKTDPGVHATLKSLSSQIETMRSPDGSKKHPARTCDDLKLCHSAKQSGEYWIDPNQGSVEDAIKVYCNMETGETCISANPSSVPRKTWWASKSPDNKPVWYGLDMNRGSQFAYGDHQSPNTAITQMTFLRLLSKEASQNITYICKNSVGYMDDQAKNLKKAVVLKGANDLDIKAEGNIRFRYIVLQDTCSKRNGNVGKTVFEYRTQNVARLPIIDLAPVDVGGTDQEFGVEIGPVCFV", "length": 1112, "header": "tr|A0A087WYX9-1|A0A087WYX9_HUMAN Computationally mapped isoform of Collagen type V alpha 2 chain OS=Homo sapiens OX=9606 GN=COL5A2 PE=1 SV=1 CANONICAL=P05997-1" }, "locus": { "chromosome": "2", "start_pos": 189088709, "end_pos": 189034073, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000618828.1", "url": "https://www.ensembl.org/id/ENST00000618828.1" }, { "database": "Ensembl Peptide", "id": "ENSP00000482184.1", "url": "https://www.ensembl.org/id/ENSP00000482184.1" } ] } }, { "isoform_ac": "A0A3B3IRH9-1", "url": "", "sequence": { "sequence": "MYLNRDIWKPAPCQICVCDNGAILCDKIECQDVLDCADPVTPPGECCPVCSQTPGGGNTNFGRGRKGQKGEPGLVPVVTGIRGRPGPAGPPGSQGPRGERGPKGRPGPRGPQGIDGEPGVPGQPGAPGPPGHPSHPGPDGLSRPFSAQMAGLDEKSGLGSQVGLMPGSVGPVGPRGPQGLQGQQGGAGPTGPPGEPGDPGPMGPIGSRGPEGPPGK", "length": 216, "header": "tr|A0A3B3IRH9-1|A0A3B3IRH9_HUMAN Computationally mapped isoform of Collagen type V alpha 2 chain OS=Homo sapiens OX=9606 GN=COL5A2 PE=1 SV=1 CANONICAL=P05997-1" }, "locus": { "chromosome": "2", "start_pos": 189110408, "end_pos": 189085172, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000649966.1", "url": "https://www.ensembl.org/id/ENST00000649966.1" }, { "database": "Ensembl Peptide", "id": "ENSP00000496785.1", "url": "https://www.ensembl.org/id/ENSP00000496785.1" } ] } }, { "isoform_ac": "P05997-1", "url": "", "sequence": { "sequence": "MMANWAEARPLLILIVLLGQFVSIKAQEEDEDEGYGEEIACTQNGQMYLNRDIWKPAPCQICVCDNGAILCDKIECQDVLDCADPVTPPGECCPVCSQTPGGGNTNFGRGRKGQKGEPGLVPVVTGIRGRPGPAGPPGSQGPRGERGPKGRPGPRGPQGIDGEPGVPGQPGAPGPPGHPSHPGPDGLSRPFSAQMAGLDEKSGLGSQVGLMPGSVGPVGPRGPQGLQGQQGGAGPTGPPGEPGDPGPMGPIGSRGPEGPPGKPGEDGEPGRNGNPGEVGFAGSPGARGFPGAPGLPGLKGHRGHKGLEGPKGEVGAPGSKGEAGPTGPMGAMGPLGPRGMPGERGRLGPQGAPGQRGAHGMPGKPGPMGPLGIPGSSGFPGNPGMKGEAGPTGARGPEGPQGQRGETGPPGPVGSPGLPGAIGTDGTPGAKGPTGSPGTSGPPGSAGPPGSPGPQGSTGPQGIRGQPGDPGVPGFKGEAGPKGEPGPHGIQGPIGPPGEEGKRGPRGDPGTVGPPGPVGERGAPGNRGFPGSDGLPGPKGAQGERGPVGSSGPKGSQGDPGRPGEPGLPGARGLTGNPGVQGPEGKLGPLGAPGEDGRPGPPGSIGIRGQPGSMGLPGPKGSSGDPGKPGEAGNAGVPGQRGAPGKDGEVGPSGPVGPPGLAGERGEQGPPGPTGFQGLPGPPGPPGEGGKPGDQGVPGDPGAVGPLGPRGERGNPGERGEPGITGLPGEKGMAGGHGPDGPKGSPGPSGTPGDTGPPGLQGMPGERGIAGTPGPKGDRGGIGEKGAEGTAGNDGARGLPGPLGPPGPAGPTGEKGEPGPRGLVGPPGSRGNPGSRGENGPTGAVGFAGPQGPDGQPGVKGEPGEPGQKGDAGSPGPQGLAGSPGPHGPNGVPGLKGGRGTQGPPGATGFPGSAGRVGPPGPAGAPGPAGPLGEPGKEGPPGLRGDPGSHGRVGDRGPAGPPGGPGDKGDPGEDGQPGPDGPPGPAGTTGQRGIVGMPGQRGERGMPGLPGPAGTPGKVGPTGATGDKGPPGPVGPPGSNGPVGEPGPEGPAGNDGTPGRDGAVGERGDRGDPGPAGLPGSQGAPGTPGPVGAPGDAGQRGDPGSRGPIGPPGRAGKRGLPGPQGPRGDKGDHGDRGDRGQKGHRGFTGLQGLPGPPGPNGEQGSAGIPGPFGPRGPPGPVGPSGKEGNPGPLGPIGPPGVRGSVGEAGPEGPPGEPGPPGPPGPPGHLTAALGDIMGHYDESMPDPLPEFTEDQAAPDDKNKTDPGVHATLKSLSSQIETMRSPDGSKKHPARTCDDLKLCHSAKQSGEYWIDPNQGSVEDAIKVYCNMETGETCISANPSSVPRKTWWASKSPDNKPVWYGLDMNRGSQFAYGDHQSPNTAITQMTFLRLLSKEASQNITYICKNSVGYMDDQAKNLKKAVVLKGANDLDIKAEGNIRFRYIVLQDTCSKRNGNVGKTVFEYRTQNVARLPIIDLAPVDVGGTDQEFGVEIGPVCFV", "length": 1499, "header": "sp|P05997-1|CO5A2_HUMAN Isoform 1 of Collagen alpha-2(V) chain OS=Homo sapiens OX=9606 GN=COL5A2 PE=1 SV=3 CANONICAL=P05997-1" }, "locus": { "chromosome": "2", "start_pos": 189179604, "end_pos": 189034073, "strand": "+", "evidence": [ { "database": "Ensembl Transcript", "id": "ENST00000374866.9", "url": "https://www.ensembl.org/id/ENST00000374866.9" }, { "database": "Ensembl Peptide", "id": "ENSP00000364000.3", "url": "https://www.ensembl.org/id/ENSP00000364000.3" } ] } } ], "glycosylation": [ { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "T", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "start_pos": 1015, "start_aa": "Thr", "end_pos": 1015, "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1015", "evidence": [ { "id": "P05997", "database": "UniCarbKB", "url": "" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] }, { "glytoucan_ac": "G84452RH", "type": "N-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "N", "relation": "attached", "comment": "", "start_pos": 1262, "start_aa": "Asn", "end_pos": 1262, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1262", "evidence": [ { "id": "1136", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1136" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "site_category": "reported", "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "start_pos": 1262, "start_aa": "Asn", "end_pos": 1262, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1262", "evidence": [ { "id": "P05997", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P05997#ptm_processing" } ] }, { "glytoucan_ac": "G05724UK", "type": "N-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "N", "relation": "attached", "comment": "", "start_pos": 1400, "start_aa": "Asn", "end_pos": 1400, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1400", "evidence": [ { "id": "1136", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1136" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "N", "relation": "attached", "comment": "", "start_pos": 1400, "start_aa": "Asn", "end_pos": 1400, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1400", "evidence": [ { "id": "1136", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1136" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "G23294PN", "type": "N-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "N", "relation": "attached", "comment": "", "start_pos": 1400, "start_aa": "Asn", "end_pos": 1400, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1400", "evidence": [ { "id": "1136", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1136" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "G39188ZX", "type": "N-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "N", "relation": "attached", "comment": "", "start_pos": 1400, "start_aa": "Asn", "end_pos": 1400, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1400", "evidence": [ { "id": "1136", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1136" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "G70101JE", "type": "N-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "N", "relation": "attached", "comment": "", "start_pos": 1400, "start_aa": "Asn", "end_pos": 1400, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1400", "evidence": [ { "id": "1136", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1136" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "site_category": "reported", "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "start_pos": 1400, "start_aa": "Asn", "end_pos": 1400, "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1400", "evidence": [ { "id": "P05997", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P05997#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" } ] }, { "glytoucan_ac": "G43417UB", "type": "O-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "S", "relation": "attached", "comment": "", "start_pos": 188, "start_aa": "Ser", "end_pos": 188, "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser188", "evidence": [ { "id": "P05997", "database": "UniCarbKB", "url": "" }, { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" } ] }, { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "site_category": "reported_with_glycan", "site_seq": "GTQGPPGATGFPGSAGR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "start_pos": 900, "start_aa": "Gly", "end_pos": 916, "end_aa": "Arg", "evidence": [ { "id": "P05997", "database": "UniCarbKB", "url": "" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] }, { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "site_category": "reported_with_glycan", "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "start_pos": 913, "start_aa": "Ser", "end_pos": 913, "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser913", "evidence": [ { "id": "P05997", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05997" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "phosphorylation": [], "glycation": [], "keywords": [ "glycoprotein", "glycoprotein_reported_with_glycan", "glycoprotein_reported" ], "publication": [ { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "journal": "EMBO J", "date": "2013", "authors": "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "evidence": [ { "database": "UniCarbKB", "id": "P05997", "url": "" } ], "reference": [ { "type": "DOI", "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] }, { "title": "Binding of the G domains of laminin alpha1 and alpha2 chains and perlecan to heparin, sulfatides, alpha-dystroglycan and several extracellular matrix proteins.", "journal": "The EMBO journal", "date": "1999", "authors": "Talts JF, Andac Z, Gohring W, Brancaccio A, Timpl R", "evidence": [ { "database": "Reactome", "id": "R-HSA-3000178", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3000178" } ], "reference": [ { "type": "PubMed", "id": "10022829", "url": "https://glygen.org/publication/PubMed/10022829" } ] }, { "title": "Antiangiogenic activity of restin, NC10 domain of human collagen XV: comparison to endostatin.", "journal": "Biochemical and biophysical research communications", "date": "1999", "authors": "Ramchandran R, Dhanabal M, Volk R, Waterman MJ, Segal M, Lu H, Knebelmann B, Sukhatme VP", "evidence": [ { "database": "Reactome", "id": "R-HSA-1442490", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1442490" } ], "reference": [ { "type": "PubMed", "id": "10049780", "url": "https://glygen.org/publication/PubMed/10049780" } ] }, { "title": "The integrin alpha9beta1 mediates adhesion to activated endothelial cells and transendothelial neutrophil migration through interaction with vascular cell adhesion molecule-1.", "journal": "The Journal of cell biology", "date": "1999", "authors": "Taooka Y, Chen J, Yednock T, Sheppard D", "evidence": [ { "database": "Reactome", "id": "R-HSA-216083", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-216083" } ], "reference": [ { "type": "PubMed", "id": "10209034", "url": "https://glygen.org/publication/PubMed/10209034" } ] }, { "title": "Agrin in Alzheimer's disease: altered solubility and abnormal distribution within microvasculature and brain parenchyma.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "1999", "authors": "Donahue JE, Berzin TM, Rafii MS, Glass DJ, Yancopoulos GD, Fallon JR, Stopa EG", "evidence": [ { "database": "Reactome", "id": "R-HSA-3000178", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3000178" } ], "reference": [ { "type": "PubMed", "id": "10339611", "url": "https://glygen.org/publication/PubMed/10339611" } ] }, { "title": "Alpha 2 beta 1 integrin mediates dermal fibroblast attachment to type VII collagen via a 158-amino-acid segment of the NC1 domain.", "journal": "Experimental cell research", "date": "1999", "authors": "Chen M, O'Toole EA, Li YY, Woodley DT", "evidence": [ { "database": "Reactome", "id": "R-HSA-216083", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-216083" } ], "reference": [ { "type": "PubMed", "id": "10366422", "url": "https://glygen.org/publication/PubMed/10366422" } ] }, { "title": "The leukocyte integrin alpha D beta 2 binds VCAM-1: evidence for a binding interface between I domain and VCAM-1.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1999", "authors": "Van der Vieren M, Crowe DT, Hoekstra D, Vazeux R, Hoffman PA, Grayson MH, Bochner BS, Gallatin WM, Staunton DE", "evidence": [ { "database": "Reactome", "id": "R-HSA-216083", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-216083" } ], "reference": [ { "type": "PubMed", "id": "10438935", "url": "https://glygen.org/publication/PubMed/10438935" } ] }, { "title": "Mammalian BMP-1/Tolloid-related metalloproteinases, including novel family member mammalian Tolloid-like 2, have differential enzymatic activities and distributions of expression relevant to patterning and skeletogenesis.", "journal": "Developmental biology", "date": "1999", "authors": "Scott IC, Blitz IL, Pappano WN, Imamura Y, Clark TG, Steiglitz BM, Thomas CL, Maas SA, Takahara K, Cho KW, Greenspan DS", "evidence": [ { "database": "Reactome", "id": "R-HSA-1650814", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1650814" } ], "reference": [ { "type": "PubMed", "id": "10479448", "url": "https://glygen.org/publication/PubMed/10479448" } ] }, { "title": "Mechanism of action and in vivo role of platelet-derived growth factor.", "journal": "Physiological reviews", "date": "1999", "authors": "Heldin CH, Westermark B", "evidence": [ { "database": "Reactome", "id": "R-HSA-186797", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-186797" } ], "reference": [ { "type": "PubMed", "id": 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"Mutations of the alpha2(V) chain of type V collagen impair matrix assembly and produce Ehlers-Danlos syndrome type I.", "journal": "Hum. Mol. Genet.", "date": "1998", "authors": "Michalickova K, Susic M, Willing M C, Wenstrup R J, Cole W G", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "reference": [ { "type": "PubMed", "id": "9425231", "url": "https://glygen.org/publication/PubMed/9425231" } ] }, { "title": "The alphavbeta5 integrin functions as an endocytic receptor for vitronectin.", "journal": "Journal of cell science", "date": "1998", "authors": "Memmo LM, McKeown-Longo P", "evidence": [ { "database": "Reactome", "id": "R-HSA-216083", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-216083" } ], "reference": [ { "type": "PubMed", "id": "9443892", "url": "https://glygen.org/publication/PubMed/9443892" } ] }, { "title": "Protein disulfide isomerase acts as a molecular chaperone during the assembly of procollagen.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Wilson R, Lees JF, Bulleid NJ", "evidence": [ { "database": "Reactome", "id": "R-HSA-1650814", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1650814" } ], "reference": [ { "type": "PubMed", "id": "9545296", "url": "https://glygen.org/publication/PubMed/9545296" } ] }, { "title": "Thiol-independent interaction of protein disulphide isomerase with type X collagen during intra-cellular folding and assembly.", "journal": "The Biochemical journal", "date": "1998", "authors": "McLaughlin SH, Bulleid NJ", "evidence": [ { "database": "Reactome", "id": "R-HSA-1650814", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1650814" } ], "reference": [ { "type": "PubMed", "id": "9560306", "url": "https://glygen.org/publication/PubMed/9560306" } ] }, { "title": "Identification of the ligand binding site for the integrin alpha9 beta1 in the third fibronectin type III repeat of tenascin-C.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Yokosaki Y, Matsuura N, Higashiyama S, Murakami I, Obara M, Yamakido M, Shigeto N, Chen J, Sheppard D", "evidence": [ { "database": "Reactome", "id": "R-HSA-216083", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-216083" } ], "reference": [ { "type": "PubMed", "id": "9565552", "url": "https://glygen.org/publication/PubMed/9565552" } ] }, { "title": "Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3)", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Valtavaara M, Szpirer C, Szpirer J, Myllyla R", "evidence": [ { "database": "Reactome", "id": "R-HSA-1650814", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1650814" } ], "reference": [ { "type": "PubMed", "id": "9582318", "url": "https://glygen.org/publication/PubMed/9582318" } ] }, { "title": "Cloning and characterization of a novel matrix metalloproteinase (MMP), CMMP, from chicken embryo fibroblasts. CMMP, Xenopus XMMP, and human MMP19 have a conserved unique cysteine in the catalytic domain.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Yang M, Kurkinen M", "evidence": [ { "database": "Reactome", "id": "R-HSA-1442490", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1442490" } ], "reference": [ { "type": "PubMed", "id": "9651395", "url": "https://glygen.org/publication/PubMed/9651395" } ] }, { "title": "The discoidin domain receptor tyrosine kinases are activated by collagen.", "journal": "Molecular cell", "date": "1997", "authors": "Vogel W, Gish GD, Alves F, Pawson T", "evidence": [ { "database": "Reactome", "id": "R-HSA-3000171", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3000171" } ], "reference": [ { "type": "PubMed", "id": "9659899", "url": "https://glygen.org/publication/PubMed/9659899" } ] }, { "title": "An orphan receptor tyrosine kinase family whose members serve as nonintegrin collagen receptors.", "journal": "Molecular cell", "date": "1997", "authors": "Shrivastava A, Radziejewski C, Campbell E, Kovac L, McGlynn M, Ryan TE, Davis S, Goldfarb MP, Glass DJ, Lemke G, Yancopoulos GD", "evidence": [ { "database": "Reactome", "id": "R-HSA-3000171", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3000171" } ], "reference": [ { "type": "PubMed", "id": "9659900", "url": "https://glygen.org/publication/PubMed/9659900" } ] }, { "title": "Cartilage oligomeric matrix protein shows high affinity zinc-dependent interaction with triple helical collagen.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Rosenberg K, Olsson H, Morgelin M, Heinegard D", "evidence": [ { "database": "Reactome", "id": "R-HSA-3000178", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3000178" } ], "reference": [ { "type": "PubMed", "id": "9685393", "url": "https://glygen.org/publication/PubMed/9685393" } ] }, { "title": "Signal transduction via platelet-derived growth factor receptors.", "journal": "Biochimica et biophysica acta", "date": "1998", "authors": "Heldin CH, Ostman A, Ronnstrand L", "evidence": [ { "database": "Reactome", "id": "R-HSA-186797", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-186797" } ], "reference": [ { "type": "PubMed", "id": "9739761", "url": "https://glygen.org/publication/PubMed/9739761" } ] }, { "title": "A single base mutation in COL5A2 causes Ehlers-Danlos syndrome type II.", "journal": "Journal of medical genetics", "date": "1998", "authors": "Richards AJ, Martin S, Nicholls AC, Harrison JB, Pope FM, Burrows NP", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "reference": [ { "type": "PubMed", "id": "9783710", "url": "https://glygen.org/publication/PubMed/9783710" } ] }, { "title": "Interaction of BP180 (type XVII collagen) and alpha6 integrin is necessary for stabilization of hemidesmosome structure.", "journal": "The Journal of investigative dermatology", "date": "1998", "authors": "Hopkinson SB, Findlay K, deHart GW, Jones JC", "evidence": [ { "database": "Reactome", "id": "R-HSA-2022090", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-2022090" } ], "reference": [ { "type": "PubMed", "id": "9856810", "url": "https://glygen.org/publication/PubMed/9856810" } ] }, { "title": "Effect of the interaction between fibronectin and VLA-4 on the proliferation of human B cells, especially a novel human B-cell line, OPM-3.", "journal": "British journal of haematology", "date": "1998", "authors": "Yoshida H, Nishiura T, Karasuno T, Matsumura I, Ishikawa J, Yoshimura M, Yokota T, Okajima Y, Ogawa M, Kanakura Y, Tomiyama Y, Matsuzawa Y", "evidence": [ { "database": "Reactome", "id": "R-HSA-216083", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-216083" } ], "reference": [ { "type": "PubMed", "id": "9858236", "url": "https://glygen.org/publication/PubMed/9858236" } ] }, { "title": "Tenascin-C inhibits beta1 integrin-dependent cell adhesion and neurite outgrowth on fibronectin by a disialoganglioside-mediated signaling mechanism.", "journal": "Glycobiology", "date": "1999", "authors": "Probstmeier R, Pesheva P", "evidence": [ { "database": "Reactome", "id": "R-HSA-3000178", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3000178" } ], "reference": [ { "type": "PubMed", "id": "9949188", "url": "https://glygen.org/publication/PubMed/9949188" } ] } ], "pathway": [ { "id": "hsa:1290", "name": "", "url": "https://www.genome.jp/dbget-bin/get_linkdb?-t+pathway+hsa:1290", "resource": "KEGG Pathway" }, { "id": "R-HSA-1442490", "name": "Collagen degradation", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1442490", "resource": "Reactome", "description": "Collagen degradation" }, { "id": "R-HSA-1474244", "name": "Extracellular matrix organization", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1474244", "resource": "Reactome", "description": "Extracellular matrix organization" 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"MMANWVVARPLLILFVLLGYCVSIKAQEQENDDYDEEIACTQHGQMYLNRDIWKPSPCQICVCDNGAILCDKIECQEVLNCANPVTPPGECCPACPQTSGGGDTSFGKTAQSWTKRRTRISSCCKYICVCMLYYGPPGSQGPRGDRGPKGRPGPRGPQGIDGEPGVPGQPGAPGPPGHPSHPGPDGMSRPFSAQMAGLDEKSGLGSQVGLMPGSVGPIGPRGPQGLQGQQGGVGPAGPPGEPGEPGPMGPIGARGPEGPPGKPGEDGEPGRNGNTGEVGFSGSPGARGFPGAPGLPGLKGHRGNKGLEGPKGEVGAPGAKGEAGPTGPMGAMGPLGPRGMPGERGRLGPQGAPGQRGAHGMPGKPGPMGPLGIPGSSGFPGNPGVKGEAGPTGARGPEGPQGQRGETGPPGPAGSHGLPGAVGTDGTPGAKGPTGSPGTSGPPGLAGPPGSPGPQGSTGPQGIRGQLGDPGVPGFKGEAGPKGEPGPHGIQGPIGPPGEEGKRGPRGDPGTVGPPGPMGERGAPGNRGFPGSDGLPGPKGAQGERGPIGSSGPKGGQGDPGRPGEPGLPGARGLTGNPGVQGPEGKLGPLGAPGEDGRPGPPGSIGIRGQPGSMGLPGPKGSSGDLGKPGEAGNAGVPGQRGAPGKDGEVGPSGPVGPPGLAGERGEQGPPGPTGFQGLPGPPGPPGEGGKPGDQGVPGEPGAVGPLGPRGERGNPGERGEPGITGLPGEKGMAGGHGPDGPKGNPGPTGTIGDTGPPGLQGMPGERGIAGTPGPKGDRGGVGEKGAEGTAGNDGARGLPGSLGPPGPAGPTGEKGEPGPRGLVGPPGSRGNPGSRGENGPTGAVGFAGPQGPDGQPGVKGEPGEPGQKGDAGSPGPQGLAGSPGPHGPHGVPGLKGGRGTQGPPGATGFPGSAGRVGPPGPAGAPGPAGPIGEPGKEGPPGLRGDPGSHGRVGDRGPAGPPGSPGDKGDPGEDGQPGPDGPPGPAGTTGQRGIVGMPGQRGERGMPGLPGPAGTPGKVGPTGATGDKGPPGPVGPPGSNGPVGEPGPEGPAGNDGTPGRDGAVGERGDRGDPGPAGLPGSQGAPGTPGPVGAPGDAGQRGEPGSRGPVGPPGRAGKRGLPGPQGPRGDKGDNGDRGDRGQKGHRGFTGLQGLPGPPGPNGEQGSAGIPGPFGPRGPPGPVGPSGKEGNPGLLGPIGPPGVRGSVGEAGPEGPPGEPGPPGPPGPPGHLTAALGDIMGHYDENMPDPLPEFTEDQAAPDDTNKTDPGVHATLKSLSSQIETMRSPDGSKKHPARTCDDLKLCHPTKQSGEYWIDPNQGSAEDAIKVYCNLETGETCISANPASVPRKTWWASKSPDNKPVWYGLDMNRGSQFTYGDYKSPNTAITQMTFLRLLSKEASQNLTYICKNTVGYMDDQTKNLKKAVVLKGSNDLEIKGEGNIRFRYTVLQDTCSKRNGNVGKTVFEYRTQNVARLPIIDIGPVDIGNADQEFGFEIGPVCFM", 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"length": 1497 }, "evidence": [ { "id": "45928020", "url": "http://www.informatics.jax.org/homology/45928020", "database": "MGI" }, { "id": "P05997", "url": "https://omabrowser.org/oma/group/P05997/", "database": "OMA" } ], "common_name": "Mouse" } ], "go_annotation": { "categories": [ { "name": "Cellular Component", "total": 7, "go_terms": [ { "name": "extracellular region", "id": "GO:0005576", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005576", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "extracellular space", "id": "GO:0005615", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005615", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "endoplasmic reticulum lumen", "id": "GO:0005788", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005788", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "extracellular matrix", "id": "GO:0031012", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0031012", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "collagen type XI trimer", "id": "GO:0005592", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005592", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "collagen type V trimer", "id": "GO:0005588", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005588", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "collagen-containing extracellular matrix", "id": "GO:0062023", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0062023", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" } ] }, { "name": "Biological Process", "total": 8, "go_terms": [ { "name": "extracellular matrix organization", "id": "GO:0030198", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030198", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "skeletal system development", "id": "GO:0001501", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0001501", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "collagen fibril organization", "id": "GO:0030199", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030199", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "skin development", "id": "GO:0043588", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0043588", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "ossification", "id": "GO:0001503", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0001503", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "cellular response to amino acid stimulus", "id": "GO:0071230", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0071230", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "eye morphogenesis", "id": "GO:0048592", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0048592", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "negative regulation of endodermal cell differentiation", "id": "GO:1903225", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:1903225", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" } ] }, { "name": "Molecular Function", "total": 4, "go_terms": [ { "name": "metal ion binding", "id": "GO:0046872", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0046872", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "SMAD binding", "id": "GO:0046332", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0046332", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "extracellular matrix structural constituent conferring tensile strength", "id": "GO:0030020", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0030020", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" }, { "name": "extracellular matrix structural constituent", "id": "GO:0005201", "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005201", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" } ], "pmid": "" } ] } ] }, "pro_annotation": [ { "name": "collagen alpha-2(V) chain O-glycosylated 1 (human)", "definition": "A collagen alpha-2(V) chain (human) that has been O-glycosylated at the residue equivalent to Ser-188 of the amino acid sequence represented by UniProtKB:P05997-1, in which the glycan composition is represented by GlyTouCan:G43417UB. Example: UniProtKB:P05997-1, Ser-188, MOD:00002~GNO:G43417UB. [PRO:DNx, PMID:30459171]", "evidence": [ { "id": "PR:000053569", "database": "PRO", "url": "https://proconsortium.org/app/entry/PR:000053569" } ] } ], "site_annotation": [ { "start_pos": 1262, "end_pos": 1264, "annotation": "n_glycosylation_sequon" }, { "start_pos": 1400, "end_pos": 1402, "annotation": "n_glycosylation_sequon" } ], "ptm_annotation": [ { "annotation": "Prolines at the third position of the tripeptide repeating unit (G-X-P) are hydroxylated in some or all of the chains. Probably 3-hydroxylated on Pro-919 and Pro-1156 by LEPREL1.", "evidence": [ { "database": "UniProtKB", "id": "P05997", "url": "https://www.uniprot.org/uniprot/P05997" }, { "database": "PubMed", "id": "8181482", "url": "https://glygen.org/publication/PubMed/8181482" }, { "database": "PubMed", "id": "21757687", "url": "https://glygen.org/publication/PubMed/21757687" } ] } ], "interactions": [], "reactions": [], "reaction_participants": [], "reaction_enzymes": [], "biomarkers": [], "synthesized_glycans": [], "cluster_types": [ { "name": "isoformset.uniprotkb", "label": "Isoforms" }, { "name": "homologset.oma", "label": "OMA Homologs" }, { "name": "homologset.mgi", "label": "MGI Homologs" } ], "sequence_features": { "n_linked_sites": [ 1262, 1400 ], "o_linked_sites": [ 188, 900, 913, 1015 ], "snv_sites": [ 6, 284, 592, 620, 743, 841, 1015, 1241, 1262, 1264, 1269, 1286, 1341, 1400, 1402, 1414, 1440, 1449, 1456, 1458, 1470 ], "glycation_sites": [], "phosphorylation_sites": [], "sequon_annotation_sites": [ { "start_pos": 1262, "end_pos": 1264 }, { "start_pos": 1400, "end_pos": 1402 } ] }, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 12 }, { "field": "total_sites", "count": 6 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "n_linked_glycan_sites", "count": 4 }, { "field": "o_linked_glycans", "count": 3 }, { "field": "o_linked_glycan_sites", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_pos", "start_aa", "end_pos", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 2 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_pos", "start_aa", "end_pos", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 10 }, { "field": "total_sites", "count": 6 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "n_linked_glycan_sites", "count": 2 }, { "field": "o_linked_glycans", "count": 3 }, { "field": "o_linked_glycan_sites", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_pos", "start_aa", "end_pos", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 25 }, { "field": "total_sites", "count": 21 } ], "sort_fields": [ "start_pos", "end_pos", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 12 }, { "field": "total_sites", "count": 12 } ], "sort_fields": [ "start_pos", "end_pos", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 13 }, { "field": "total_sites", "count": 11 } ], "sort_fields": [ "start_pos", "end_pos", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 265 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }